Utility of mutagenesis and next generation sequencing for accelerating the domestication of a new niche cereal

A native Australian perennial grass has been targeted for accelerated domestication utilising a combination of mutation breeding and high throughput genomics. Ecovars of Microlaena stipoides exhibit high water use efficiency and have demonstrated adaptability to a suite of abiotic stresses including drought, frost, shade, salt and acid soils. Once established, M. stipoides would be maintained as a zero-till crop which produces reasonable yields of grain of similar size, taste, texture and cooking properties as rice. Accelerated domestication primarily targeted the development of a non-shattering phenotype. Ethyl methanesulfonate was used to induce point mutations in a selected breeding line of M. stipoides with the aim of inducing a loss of function at the homologues of the qSH1 and SHA1 shattering loci identified in Oryza sativa. Amplicons of both of these loci were pooled from 109 control samples and compared with a pool of 109 potential mutant samples and a further pool of 754 potential mutants, and screened for single nucleotide polymorphisms (SNP) using next generation sequencing on the Illumina GA II platform. Putatively functional SNP were identified at both homologous loci. Forty-six elite breeding lines, of which 24 were non-shattering at the M2 generation, have been developed and are currently under cultivation for M3 phenotypic screening. It is envisaged that this methodology could be employed to accelerate the domestication of other wild grasses, which have intrinsic abiotic adaptability, as new food, fibre and fuel crops.